A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain–peptide interaction from primary sequence

Large-scale prediction of protein-protein interactions from structures

(2010) Martial Hue et al.   BMC BIOINFORMATICS

Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains

(2010) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

Novel Peptide-Mediated Interactions Derived from High-Resolution 3-Dimensional Structures

(2010) Amelie Stein et al.   PLoS Computational Biology

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Using genome-wide measurements for computational prediction of SH2–peptide interactions

(2009) Zeba Wunderlich et al.   NUCLEIC ACIDS RESEARCH

High-energy water sites determine peptide binding affinity and specificity of PDZ domains

(2009) Thijs Beuming et al.   PROTEIN SCIENCE

Rapid Evolution of Functional Complexity in a Domain Family

(2009) A. Ernst et al.   Science Signaling

The Precise Sequence of FGF Receptor Autophosphorylation Is Kinetically Driven and Is Disrupted by Oncogenic Mutations

(2009) E. D. Lew et al.   Science Signaling

Cell regulation: determined to signal discrete cooperation

(2009) Toby J. Gibson   TRENDS IN BIOCHEMICAL SCIENCES

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

(2009) Raffi Tonikian et al.   PLOS BIOLOGY

The Relative Binding Affinities of PDZ Partners for CFTR: A Biochemical Basis for Efficient Endocytic Recycling†

(2008) Patrick R. Cushing et al.   BIOCHEMISTRY

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods

(2008) Hao Zhang et al.   BIOINFORMATICS

Predicting PDZ domain–peptide interactions from primary sequences

(2008) Jiunn R Chen et al.   NATURE BIOTECHNOLOGY

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

(2008) Gal Chechik et al.   NATURE BIOTECHNOLOGY

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan

(2008) Morten Nielsen et al.   PLoS Computational Biology

Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm

(2008) Ignacio E. Sánchez et al.   PLoS Computational Biology